year 18, Issue 1 (January - February 2024)                   Iran J Med Microbiol 2024, 18(1): 41-48 | Back to browse issues page


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Fadila W, H. Wahid M, Fadilah F, Syahniar R, Krisnuhoni E, Yasmon A. Two Novel Amino Acid Insertions in the Helicobacter pylori rdxA Gene Detected in Gastric Paraffin Biopsies. Iran J Med Microbiol 2024; 18 (1) :41-48
URL: http://ijmm.ir/article-1-2179-en.html
1- Department of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
2- Department of Microbiology, Faculty of Medicine, Universitas Indonesia-Cipto Mangunkusumo Hospital, Jakarta, Indonesia
3- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
4- Department of Microbiology and Parasitology, Faculty of Medicine and Health, Universitas Muhammadiyah, Jakarta, Indonesia
5- Department of Anatomic Pathology, Faculty of Medicine, Universitas Indonesia-Cipto Mangunkusumo Hospital, Jakarta, Indonesia
6- Department of Microbiology, Faculty of Medicine, Universitas Indonesia-Cipto Mangunkusumo Hospital, Jakarta, Indonesia , andiyasmon@gmail.com
Abstract:   (389 Views)

Background and Aim: The biggest problem in the management of patients with Helicobacter pylori infections is resistance to the first-line antibiotic drug metronidazole. Several mechanisms underlie the resistance of H. pylori to metronidazole, and one of them is mutations in the rdxA gene encoding the nicotinamide adenine dinucleotide phosphate (NADPH) protein. Therefore, we characterized the rdxA gene amplified by PCR from gastric paraffin biopsies.
Materials and Methods: This is an explorative study using 34 gastric paraffin biopsies that were H. pylori positive in a real-time PCR assay. To analyze the rdxA gene, we conducted nested PCR of a gene fragment, followed by DNA sequencing to analyze amino acid changes and protein structure analysis.
Results: Of the 34 H. pylori-positive paraffin biopsies, 5 were positive for the rdxA gene fragment. The amino acid change analysis showed that the NADPH protein had substitutions, insertions, frameshifts, and premature stop codons. Two novel amino acid insertions were found. The protein structure analysis showed that the NADPH protein with substitutions had amino acid changes forming 2 pockets for active sites. The NAPDH protein with substitutions and the 2 novel insertions showed the loss of one pocket.
Conclusion: The present study reports on the genetic analysis of the rdxA gene showing DNA sequence diversity. Two amino acid insertions in the NADPH gene are a unique finding, and their effect on antibacterial-resistant phenotype needs to be investigated in future studies.

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Type of Study: Original Research Article | Subject: Antibiotic Resistance
Received: 2023/12/1 | Accepted: 2024/03/7 | ePublished: 2024/03/18

References
1. Ierardi E, Losurdo G, Mileti A, Paolillo R, Giorgio F, Principi M, Di Leo A. The puzzle of coccoid forms of Helicobacter pylori: beyond basic science. Antibiotics. 2020;9(6):293. [DOI:10.3390/antibiotics9060293] [PMID] [PMCID]
2. Svane S, Sigurdarson JJ, Finkenwirth F, Eitinger T, Karring H. Inhibition of urease activity by different compounds provides insight into the modulation and association of bacterial nickel import and ureolysis. Sci Rep. 2020;10:8503. [DOI:10.1038/s41598-020-65107-9] [PMID] [PMCID]
3. Malfertheiner P, Camargo MC, El-Omar E, Liou JM, Peek R, Schulz C, et al. Helicobacter pylori infection. Nat Rev Dis Primers. 2023;9(1):19. [DOI:10.1038/s41572-023-00431-8] [PMID]
4. Karbalaei M, Keikha M. Potential association between the hopQ alleles of Helicobacter pylori and gastrointestinal diseases: A systematic review and meta-analysis. Meta Gene. 2020;26:100816. [DOI:10.1016/j.mgene.2020.100816]
5. Quach DT, Vilaichone RK, Vu KV, Yamaoka Y, Sugano K, Mahachai V. Helicobacter pylori Infection and Related Gastrointestinal Diseases in Southeast Asian Countries: An Expert Opinion Survey. Asian Pac J Cancer Prev. 2018;19(12):3565-9. [DOI:10.31557/APJCP.2018.19.12.3565] [PMID] [PMCID]
6. Syam AF, Miftahussurur M, Makmun D, Nusi IA, Zain LH, Zulkhairi, et al. Risk Factors and Prevalence of Helicobacter pylori in Five Largest Islands of Indonesia: A Preliminary Study. PLoS One. 2015;10(11):e0140186. [DOI:10.1371/journal.pone.0140186] [PMID] [PMCID]
7. Miftahussurur M, Syam AF, Nusi IA, Makmun D, Waskito LA, Zein LH, et al. Surveillance of Helicobacter pylori Antibiotic Susceptibility in Indonesia: Different Resistance Types among Regions and with Novel Genetic Mutations. PLoS One. 2016;11(12):e0166199. [DOI:10.1371/journal.pone.0166199] [PMID] [PMCID]
8. Vilaichone RK, Quach DT, Yamaoka Y, Sugano K, Mahachai V. Prevalence and Pattern of Antibiotic Resistant Strains of Helicobacter Pylori Infection in ASEAN. Asian Pac J Cancer Prev. 2018;19(5):1411-3.
9. Spaans SK, Weusthuis RA, Van der Oost J, Kengen SW. NADPH-generating systems in bacteria and archaea. Front Microbiol. 2015;6:742. [DOI:10.3389/fmicb.2015.00742] [PMID] [PMCID]
10. Gong Y, Zhai K, Sun L, He L, Wang H, Guo Y, Zhang J. RdxA Diversity and Mutations Associated with Metronidazole Resistance of Helicobacter pylori. Microbiol Spectr. 2023;11(2):e03903-22. [DOI:10.1128/spectrum.03903-22] [PMID] [PMCID]
11. Dingsdag SA, Hunter N. Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms. J Antimicrob Chemother. 2018;73(2):265-79. [DOI:10.1093/jac/dkx351] [PMID]
12. Kwon DH, Hulten K, Kato M, Kim JJ, Lee M, El-Zaatari FAK, et al. DNA Sequence Analysis of rdxA andfrxA from 12 Pairs of Metronidazole-Sensitive and -Resistant Clinical Helicobacter pyloriIsolates. Antimicrob Agents Chemother. 2001;45(9):2609-15. [DOI:10.1128/AAC.45.9.2609-2615.2001] [PMID] [PMCID]
13. Mirzaei N, Poursina F, Moghim S, Rahimi E, Safaei HG. The mutation of the rdxA gene in metronidazole-resistant Helicobacter pylori clinical isolates. Adv Biomed Res. 2014;3:90. [DOI:10.4103/2277-9175.128469] [PMID] [PMCID]
14. Rezaei S, Talebi Bezmin Abadi A, Mohabatti Mobarez A. Metronidazole-resistant Helicobacter pylori isolates without rdxA mutations obtained from Iranian dyspeptic patients. New Microbes New Infect. 2020;34:100636. [DOI:10.1016/j.nmni.2019.100636] [PMID] [PMCID]
15. Marques B, Donato MM, Cardoso O, Luxo C, Martinho A, Almeida N. Study of rdxA and frxA genes mutations in metronidazole-resistant and -susceptible Helicobacter pylori clinical isolates from the central region of Portugal. J Glob Antimicrob Resist. 2019;17:300-4. [DOI:10.1016/j.jgar.2019.01.008] [PMID]
16. Hussein RA, Al-Ouqaili MTS, Majeed YH. Detection of Helicobacter Pylori infection by invasive and non-invasive techniques in patients with gastrointestinal diseases from Iraq: A validation study. PLoS One. 2021;16(8):e0256393. [DOI:10.1371/journal.pone.0256393] [PMID] [PMCID]
17. Menoni SMF, Bonon SHA, Zeitune JMR, Costa SCB. PCR-Based Detection and Genotyping of Helicobacter pylori in Endoscopic Biopsy Samples from Brazilian Patients. Gastroenterol Res Pract. 2013;2013:951034. [DOI:10.1155/2013/951034] [PMID] [PMCID]
18. Syahniar R, Wahid MH, Syam AF, Yasmon A. Detecting the Helicobacter pylori 16S rRNA Gene in Dyspepsia Patients Using Real-Time PCR. Acta Med Indones. 2019;51(1):34-41.
19. Ramírez-Lázaro MJ, Lario S, Casalots A, Sanfeliu E, Boix L, García-Iglesias P, et al. Real-time PCR improves Helicobacter pylori detection in patients with peptic ulcer bleeding. PLoS One. 2011;6(5):e20009. [DOI:10.1371/journal.pone.0020009] [PMID] [PMCID]
20. Begum S, Prabhu V, Mohanty V, Upadhyaya KK, Abdulla R. Unveiling the arcanum of formalin-fixed paraffin-embedded archival tissue blocks: A valuable resource for genomic DNA extraction. J Oral Maxillofac Pathol. 2022;26(2):289. [DOI:10.4103/jomfp.jomfp_424_20] [PMID] [PMCID]
21. Frazer Z, Yoo C, Sroya M, Bellora C, DeWitt BL, Sanchez I, et al. Effect of Different Proteinase K Digest Protocols and Deparaffinization Methods on Yield and Integrity of DNA Extracted From Formalin-fixed, Paraffin-embedded Tissue. J Histochem Cytochem. 2020;68(3):171-84. [DOI:10.1369/0022155420906234] [PMID] [PMCID]
22. Dupont ME, Jacobsen SB, Christiansen SNN, Tfelt-Hansen J, Smerup MH, Andersen JD, Morling N. Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels. Sci Rep. 2023;13(1):16381. [DOI:10.1038/s41598-023-43788-2] [PMID] [PMCID]
23. Dahn HA, Mountcastle J, Balacco J, Winkler S, Bista I, Schmitt AD, et al. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience. 2022;11:giac068. [DOI:10.1093/gigascience/giac068] [PMID] [PMCID]
24. Khan SS, Tijare M, Kasetty S, Jain M, Alamoudi A, Bahammam HA, et al. Evaluation and Comparison of Genomic DNA Extraction Methods and PCR Optimization on Archival Formalin-Fixed and Paraffin-Embedded Tissues of Oral Squamous Cell Carcinoma. Diagnostics (Basel). 2022;12(5):1219. [DOI:10.3390/diagnostics12051219] [PMID] [PMCID]
25. Lui Sook Y, Khoon Lin L. rdxA Gene is an Unlikely Marker for Metronidazole Resistance in the Asian Helicobacter pylori Isolates. J Microbiol Biotechnol. 2003;13(5):751-8.
26. Kim SY, Joo YM, Lee HS, Chung IS, Yoo YJ, Merrell DS, Cha JH. Genetic analysis of Helicobacter pylori clinical isolates suggests resistance to metronidazole can occur without the loss of functional rdxA. J Antibiot (Tokyo). 2009;62(1):43-50. [DOI:10.1038/ja.2008.6] [PMID]

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